VMD-L Mailing List

From: amin_at_imtech.res.in
Date: Thu Apr 26 2012 - 13:00:01 CDT

The numbers I mailed are the charges from the mol2 file and were meant to show
that they are negligible.I completely understand that -3.05311E-16 is
negligible. But the numbers from chris show that the psf file generated by vmd
has a charge of 26.67 which is much more that expexted. Thanks and regards.

Amin.

> On Thu, Apr 26, 2012 at 12:37 PM, <amin_at_imtech.res.in> wrote:
>> Thanks Chris. But that's what the problem is. This is the psf made by vmd
from
>> the parameters obtained from CGENFF. Below you can see that the mol2 file
that
>> I
>> uploaded to CGENFF had negligible charge and also if I add up the partial
charges generated by the server I get almost no charge but when vmd makes the
psf file, suddenly a whole lot of charge appers.
>> (VMD) 1 % set sel [atomselect top all]
>> atomselect0
>>>Main< (VMD) 2 % $sel get charge
>> -0.12890000641345978 -0.092000000178813934 0.15199999511241913
>> 0.011500000022351742 -0.098399996757507324 -0.62010002136230469
0.019999999552965164 0.34450000524520874 0.63910001516342163
>> 0.17700000107288361
>> 0.053599998354911804 0.15000000596046448 -0.13500000536441803
>> 0.14800000190734863 -0.14000000059604645 0.14000000059604645
>> 0.093900002539157867 -0.14000000059604645 -0.15700000524520874
>> -0.12399999797344208 0.1679999977350235 -0.42199999094009399
>> -0.58910000324249268 -0.1429000049829483 0.16899999976158142
>> 0.032800000160932541 -0.02199999988079071 -0.18400000035762787
>> 0.15999999642372131 -0.17579999566078186 0.14790000021457672
>> 0.12870000302791595
>> -0.55190002918243408 -0.15800000727176666 0.11370000243186951
>> -0.46309998631477356 0.43979999423027039 0.34650000929832458
>> -0.13930000364780426 0.096699997782707214 0.66710001230239868
>> 0.085699997842311859
>>>Main< (VMD) 3 % $sel get name
>> F1 C1 H1 N1 S1 O1 C10 H10 C11 H11 C12 H12 C13 H13 C14 H14 C15 C16 C17 C2 H2
N2
>> O2 F2 H3 C3 N3 C4 H4 N4 C5 H5 N5 C6 H6 N6 C7 H7 C8 H8 C9 H9
>>>Main< (VMD) 4 % get_total_charge
>> 0.0019999807700514793
>
> this is not "a lot". this is "nothing".
> please keep in mind that VMD uses
> single precision floating point numbers
> internally and not all fractions can be
> perfectly well represented in floating point.
> you can easily tell from the individual
> charges, since Tcl intermittently converts
> all floating point numbers to double
> precision before printing them.
> single precision floating point has only
> 7 digits accuracy to begin with and if
> you sum up numbers of varying magnitude
> that drops to less.
>
> axel.
>
>> From rtf file prepared using CGENFF:
>> Charge
>> -0.202
>> -0.171
>> 0.115
>> 0.178
>> -0.162
>> -0.51
>> -0.017
>> 0.319
>> 0.501
>> 0.115
>> 0.145
>> 0.194
>> -0.18
>> 0.194
>> -0.089
>> 0.115
>> 0.116
>> -0.089
>> -0.18
>> -0.099
>> 0.115
>> -0.634
>> -0.524
>> -0.202
>> 0.187
>> 0.071
>> -0.024
>> -0.136
>> 0.194
>> -0.357
>> 0.129
>> 0.09
>> -0.452
>> -0.095
>> 0.09
>> -0.473
>> 0.739
>> 0.312
>> -0.053
>> 0.09
>> 0.55
>> 0.09
>> Sum=-3.05311E-16
>> Any help would be highly appreciated.
>> Thanks.
>> Amin.
>>> You need to examine your partial charges.  See below:
>>> Best,
>>> Chris
>>>>Main< (dld) 4 % set sel [atomselect top all]
>>> atomselect1
>>>>Main< (dld) 5 % $sel get charge
>>> -0.20200000703334808 1.0 0.11500000208616257 1.0 -0.16200000047683716
-0.5099999904632568 -0.017000000923871994 0.3190000057220459
>>> 0.5009999871253967 0.11500000208616257 1.0 0.1940000057220459 1.0
0.1940000057220459 1.0 0.11500000208616257 6.0 1.0 1.0 1.0
>>> 0.11500000208616257 0.0 -0.5239999890327454 -0.20200000703334808
0.18700000643730164 1.0 0.0 1.0 0.1940000057220459 0.0 6.0
>>> 0.09000000357627869 -0.4519999921321869 1.0 0.09000000357627869
-0.4729999899864197 3.0 0.31200000643730164 -0.05299999937415123
0.09000000357627869 0.550000011920929 0.09000000357627869
>>>>Main< (dld) 6 % $sel get name
>>> F1 C1 H1 N1 S1 O1 C10 H10 C11 H11 C12 H12 C13 H13 C14 H14 C15 C16 C17 C2 H2
N2 O2 F2 H3 C3 N3 C4 H4 N4 C5 H5 N5 C6 H6 N6 C7 H7 C8 H8 C9 H9
>>>>Main< (dld) 7 % get_total_charge
>>> 26.676000081002712
>>>>Main< (dld) 8 %
>>> On Thu, Apr 26, 2012 at 4:42 AM,  <amin_at_imtech.res.in> wrote:
>>>> Dear all,
>>>>     I am trying to generate the psf file for a small molecule using parameters
>>>> generated by CGENFF but I am getting very high non integral charges. I am
using the command "vmd -dispdev text -e ign.pgn". I have attached the
required files. Can someone please help me with this?
>>>> Warm Regards.
>>>> Amin.
>>>> ______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036
>>>> दूरभाष/EPABX :0172 6665 201-202
>>> --
>>> Chris Harrison, Ph.D.
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Theoretical and Computational Biophysics Group
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>> http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078
>> ______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute
of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए,
चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>

______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202